{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14065"],"description":["Proof of principle and optimization experiment on 10X-based-iPS2-seq was performed in two experiments:  The first explorative experiment (H001AS5) was performed on two batches of hPSC and hPSC-derived cardiomyocytes at day 23 and pooled together. hPSC were not treated with Tetracycline or primed for this experiment. Tetracycline has been administered throughout the differentiation. All batches were filtered and counted by a hemocytometer with trypan blue to assess vitality (all over 95% vital); then, they were pooled in the same tube before loading the 10X chip. hPSC and hPSC-derived cells were loaded on different days on separate 10X chips G as 16000 cells aiming as target cell recovery of 10000.   The second exploratory experiment (H001AS7) is a time course from Day 0 to Day 12. Day 0 hPSC were primed and treated with Tetracycline 5 days prior library preparation. Then Day 2, Day 6 and Day 12 were treated with Tetracycline throughout and 5 day prior cardiac differentation.  Sequencing has been performed for H001AS5 on a Illumina NextSeq 500 using two High Output Kits v2.5 (150 Cycles), for H001AS8 on a NextSeq 2000 on P3 Illumina kit 100 cycles. Sequencing run: Read1, 28 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 90 cycles."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Single cell suspension obtained after harvesting cells with versene.","Library Construction - 10X user guide CG00315 Rev E for the cDNA and library construction of the gex library. The Barcode library follows the iPS2-seq protocol enrichment with a custom primer on the TET repressor.","Sequencing - Nextseq 500 high output 75 cycles and Nextseq 2000 P3 kit 100 cycles. Sequencing run: Read1, 28 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 90 cycles.","Nucleic Acid Extraction - 10X protocol with 10X user guide CG00315 Rev E. 1.6 x 10^4 cells were loaded on a 10X chip G of a 10X 3' v3 kit."],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data Transformation - The cell annotation file (2D_iPS2seq10X_monocle_cell_info.txt) can be used to further select the cells with associated barcode and with information about where cells clones are coming from Day 0 hPSC stage.","Data Transformation - The complete cds file is atached and it can be open with monocle 3 after reading it into R with the readRDS() function in R.","Data Transformation - shRNA_ID file is atached and can be used as further annotaion file for the shRNA. It can also be used to feed CatcheR with the shRNA barcode information."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"additional_accession":["ERP160151"],"pubmed_authors":["Elisa Balmas"]},"is_claimable":false,"name":"Proof of principle for iPS2-10X-seq: timecourse experiment during 2D cardiac differentiation","description":"Proof of principle and optimization experiment on 10X-based-iPS2-seq was performed in two experiments:  The first explorative experiment (H001AS5) was performed on two batches of hPSC and hPSC-derived cardiomyocytes at day 23 and pooled together. hPSC were not treated with Tetracycline or primed for this experiment. Tetracycline has been administered throughout the differentiation. All batches were filtered and counted by a hemocytometer with trypan blue to assess vitality (all over 95% vital); then, they were pooled in the same tube before loading the 10X chip. hPSC and hPSC-derived cells were loaded on different days on separate 10X chips G as 16000 cells aiming as target cell recovery of 10000.   The second exploratory experiment (H001AS7) is a time course from Day 0 to Day 12. Day 0 hPSC were primed and treated with Tetracycline 5 days prior library preparation. Then Day 2, Day 6 and Day 12 were treated with Tetracycline throughout and 5 day prior cardiac differentation.  Sequencing has been performed for H001AS5 on a Illumina NextSeq 500 using two High Output Kits v2.5 (150 Cycles), for H001AS8 on a NextSeq 2000 on P3 Illumina kit 100 cycles. Sequencing run: Read1, 28 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 90 cycles.","dates":{"release":"2025-10-27T00:00:00Z","modification":"2025-10-27T09:34:28.367Z","creation":"2024-05-10T17:18:57.555Z"},"accession":"E-MTAB-14065","cross_references":{"ENA":["ERP160151"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}